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After applying a simple reaction I am getting the following warning message:

product 1 has no mapped atoms.

I am guessing that has something to do with atoms mapping after reaction, but I am including and index to the smarts formula to avoid this allowing RDKit to know what to do with the reactants I provide, but I cannot figure out what this warning means.

My approach so far:

rxn = AllChem.ReactionFromSmarts('[Ch:1]-[C+1:2]>>[C:1]=[C+0:2].[H+]')
ps = rxn.RunReactants((Chem.MolFromSmiles('C/C1=C\\C[C@H]([C+](C)C)CC/C(C)=C/CC1'),))

Which leads me to the following warning:

product 1 has no mapped atoms.

When checking products and its smiles I can't see anything strange that can be related to the warning.

Chem.MolToSmiles(ps[0][0])
Out[16]: 'CC(C)=[C@H]1C/C=C(\\C)CC/C=C(\\C)CC1'
Chem.MolToSmiles(ps[1][0])
Out[17]: 'C=C(C)[C@H]1C/C=C(\\C)CC/C=C(\\C)CC1'

Any hints?

Fence
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    The reason is that your product [H+] is not mapped in the reactants, whereas your other reactants are mapped (:1, :2). If you remove your [H+] product from the reaction you can see that the warning is not raised – Oliver Scott Apr 10 '19 at 17:01
  • Yes, I just realized. Thank you very much Oliver :) – Fence Apr 11 '19 at 11:25

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